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The JAXP interface specifies that disable-output-escaping requests are passed in this way from the XSLT transformer to a user-written ContentHandler. This will only happen if you don't serialize the output directly. It's best not to use d-o-e unless you are serializing the output (actually, it's best not to use it at all).

disable-output-escaping is an instruction to the serializer, that is the component that turns the result tree into lexical XML. If your result is not lexical XML but a DOM4J DocumentResult, then d-o-e has no meaning. The XSLT 2.0 spec says that in such cases it should be ignored. But the JAXP spec takes into account that when you send to a ContentHandler, the ContentHandler might be acting as a serializer and might want to know about the request to disable-output-escaping. So it defines this processing instruction to convey the request.

Why are you generating the script element as text, rather than as a regular element node? This is the root of your trouble: you're thinking in terms of generating lexical XML rather than generating a result tree.